Address additional lints, CHECK issues

Author: brookslogan

Diff for: R/archive.R

@@ -382,7 +382,7 @@ validate_epi_archive <- function(x) {
 #'   would be `key(DT)`.
 #' @param abs_tol numeric, >=0; absolute tolerance to use on numeric measurement
 #'   columns when determining whether something can be compactified away; see
-#'   [`is_locf`]
+#'   [`vec_approx_equal`]
 #'
 #' @importFrom data.table is.data.table key
 #' @importFrom dplyr arrange filter

Diff for: R/epi_slide_opt_archive.R

@@ -40,7 +40,11 @@
 #'   epi_slide_opt_archive_one_epikey("value", f, "data.table", 2L, 0L, "day", "slide_value")
 #'
 #' @keywords internal
-epi_slide_opt_archive_one_epikey <- function(updates, in_colnames, f_dots_baked, f_from_package, before, after, time_type, out_colnames) {
+epi_slide_opt_archive_one_epikey <- function(
+    updates,
+    in_colnames,
+    f_dots_baked, f_from_package, before, after, time_type,
+    out_colnames) {
   # TODO check for col name clobbering
   unit_step <- unit_time_delta(time_type)
   prev_inp_snapshot <- NULL
@@ -61,7 +65,7 @@ epi_slide_opt_archive_one_epikey <- function(updates, in_colnames, f_dots_baked,
       # If the input had updates in the range t1..t2, this could produce changes
       # in slide outputs in the range t1-after..t2+before, and to compute those
       # slide values, we need to look at the input snapshot from
-      # t1-after-before..t2+before+after.
+      # t1-after-before..t2+before+after. nolint: commented_code_linter
       inp_update_t_min <- min(inp_update$time_value)
       inp_update_t_max <- max(inp_update$time_value)
       slide_t_min <- inp_update_t_min - (before + after) * unit_step
@@ -78,7 +82,8 @@ epi_slide_opt_archive_one_epikey <- function(updates, in_colnames, f_dots_baked,
     if (f_from_package == "data.table") {
       for (col_i in seq_along(in_colnames)) {
         if (before == Inf) {
-          slide[[out_colnames[[col_i]]]] <- f_dots_baked(slide[[in_colnames[[col_i]]]], seq_len(slide_nrow), adaptive = TRUE)
+          slide[[out_colnames[[col_i]]]] <-
+            f_dots_baked(slide[[in_colnames[[col_i]]]], seq_len(slide_nrow), adaptive = TRUE)
         } else {
           out_col <- f_dots_baked(slide[[in_colnames[[col_i]]]], before + after + 1L)
           if (after != 0L) {
@@ -158,7 +163,10 @@ epi_slide_opt.epi_archive <-
         purrr::partial(.f, ...)
       }
     col_names_quo <- enquo(.col_names)
-    names_info <- across_ish_names_info(.x$DT, time_type, col_names_quo, .f_info$namer, .window_size, .align, .prefix, .suffix, .new_col_names)
+    names_info <- across_ish_names_info(
+      .x$DT, time_type, col_names_quo, .f_info$namer,
+      .window_size, .align, .prefix, .suffix, .new_col_names
+    )
     window_args <- get_before_after_from_window(.window_size, .align, time_type)
     if (!is.null(.ref_time_values)) {
       cli_abort("epi_slide.epi_archive does not support the `.ref_time_values` argument")
@@ -187,7 +195,12 @@ epi_slide_opt.epi_archive <-
           nest(.by = version, .key = "subtbl") %>%
           arrange(version)
         # TODO move nesting inside the helper?
-        res <- epi_slide_opt_archive_one_epikey(group_updates, names_info$input_col_names, .f_dots_baked, .f_info$from_package, window_args$before, window_args$after, time_type, names_info$output_col_names) %>%
+        res <- epi_slide_opt_archive_one_epikey(
+          group_updates,
+          names_info$input_col_names,
+          .f_dots_baked, .f_info$from_package, window_args$before, window_args$after, time_type,
+          names_info$output_col_names
+        ) %>%
           list_rbind()
         if (use_progress) cli::cli_progress_update(id = progress_bar_id)
         res

Diff for: R/epi_slide_opt_edf.R

@@ -81,7 +81,8 @@ upstream_slide_f_info <- function(.f) {
 #'   `names(.x)`; and `output_colnames`, chr, same length as `input_col_names`
 #'
 #' @keywords internal
-across_ish_names_info <- function(.x, time_type, col_names_quo, .f_namer, .window_size, .align, .prefix, .suffix, .new_col_names) {
+across_ish_names_info <- function(.x, time_type, col_names_quo, .f_namer,
+                                  .window_size, .align, .prefix, .suffix, .new_col_names) {
   # The position of a given column can be differ between input `.x` and
   # `.data_group` since the grouping step by default drops grouping columns.
   # To avoid rerunning `eval_select` for every `.data_group`, convert
@@ -151,10 +152,10 @@ across_ish_names_info <- function(.x, time_type, col_names_quo, .f_namer, .windo
   }
   output_col_names <- .new_col_names
 
-  return(list(
+  list(
     input_col_names = input_col_names,
     output_col_names = output_col_names
-  ))
+  )
 }
 
 #' Optimized slide functions for common cases
@@ -417,7 +418,10 @@ epi_slide_opt.epi_df <- function(.x, .col_names, .f, ...,
   window_args <- get_before_after_from_window(.window_size, .align, time_type)
 
   # Handle output naming:
-  names_info <- across_ish_names_info(.x, time_type, col_names_quo, f_info$namer, .window_size, .align, .prefix, .suffix, .new_col_names)
+  names_info <- across_ish_names_info(
+    .x, time_type, col_names_quo, f_info$namer,
+    .window_size, .align, .prefix, .suffix, .new_col_names
+  )
   input_col_names <- names_info$input_col_names
   output_col_names <- names_info$output_col_names
 

Diff for: R/patch.R

@@ -12,9 +12,11 @@
 #' @param na_equal should `NA`s be considered equal to each other? (In
 #'   epiprocess, we usually want this to be `TRUE`, but that doesn't match the
 #'   [`vctrs::vec_equal()`] default, so this is mandatory.)
+#' @param .ptype as in [`vctrs::vec_equal()`].
+#' @param ... should be empty (it's here to force later arguments to be passed
+#'   by name)
 #' @param abs_tol absolute tolerance; will be used for bare numeric `vec1`,
 #'   `vec2`, or any such columns within `vec1`, `vec2` if they are data frames.
-#' @param .ptype as in [`vctrs::vec_equal()`].
 #' @param inds1,inds2 optional (row) indices into vec1 and vec2 compatible with
 #'   [`vctrs::vec_slice()`]; output should be consistent with `vec_slice`-ing to
 #'   these indices beforehand, but can give faster computation if `vec1` and
@@ -205,7 +207,9 @@ tbl_diff2 <- function(earlier_snapshot, later_tbl,
     cli_abort("`ukey_names` must be a subset of column names")
   }
   later_format <- arg_match0(later_format, c("snapshot", "update"))
-  if (!(is.vector(compactify_abs_tol, mode = "numeric") && length(compactify_abs_tol) == 1L && compactify_abs_tol >= 0)) {
+  if (!(is.vector(compactify_abs_tol, mode = "numeric") &&
+    length(compactify_abs_tol) == 1L && # nolint:indentation_linter
+    compactify_abs_tol >= 0)) {
     # Give a specific message:
     assert_numeric(compactify_abs_tol, lower = 0, any.missing = FALSE, len = 1L)
     # Fallback e.g. for invalid classes not caught by assert_numeric:
@@ -279,7 +283,7 @@ tbl_diff2 <- function(earlier_snapshot, later_tbl,
   if (later_format == "update") {
     # Cases 4. and 5.:
     combined_tbl <- combined_tbl[combined_from_later & !combined_compactify_away, ]
-  } else { # later_format == "snapshot"
+  } else { # later_format is "snapshot"
     # Which rows from combined are in case 1.?
     combined_is_deletion <- vec_rep_each(c(TRUE, FALSE), c(earlier_n, later_n))
     combined_is_deletion[ukey_repeat_first_i] <- FALSE

Diff for: man/apply_compactify.Rd

@@ -220,5 +220,13 @@ test_that("`epi_archive` rejects dataframes where time_value and version columns
 test_that("is_locf replacement works as expected", {
   vec <- c(1, 1, 1e-10, 1.1e-10, NA, NA, NaN, NaN)
   is_repeated <- c(0, 1, 0, 1, 0, 1, 1, 1)
-  expect_equal(c(FALSE, vec_approx_equal(head(vec, -1L), tail(vec, -1L), na_equal = TRUE, abs_tol = .Machine$double.eps^0.5)), as.logical(is_repeated))
+  expect_equal(
+    c(
+      FALSE,
+      vec_approx_equal(head(vec, -1L), tail(vec, -1L),
+        na_equal = TRUE, abs_tol = .Machine$double.eps^0.5
+      )
+    ),
+    as.logical(is_repeated)
+  )
 })

Diff for: man/vec_approx_equal.Rd

@@ -159,7 +159,9 @@ test_that("epi_slide_opt.epi_archive gives expected results on example data; als
 
   mini_case_death_rate_archive_time_gen <- system.time(
     mini_case_death_rate_archive_expected <- mini_case_death_rate_archive %>%
-      epix_slide(~ .x %>% epi_slide_opt(case_rate, frollmean, .window_size = 7)) %>%
+      epix_slide(
+        ~ .x %>% epi_slide_opt(case_rate, frollmean, .window_size = 7)
+      ) %>%
       select(names(mini_case_death_rate_archive$DT), everything()) %>%
       as_epi_archive()
   )
@@ -205,7 +207,9 @@ test_that("epi_slide_opt.epi_archive gives expected results on example data; als
 
   archive_cases_dv_subset_time_gen <- system.time(
     archive_cases_dv_subset_expected <- archive_cases_dv_subset %>%
-      epix_slide(~ .x %>% epi_slide_opt(percent_cli, frollmean, .window_size = 7)) %>%
+      epix_slide(
+        ~ .x %>% epi_slide_opt(percent_cli, frollmean, .window_size = 7)
+      ) %>%
       select(geo_value, time_value, version, everything()) %>%
       as_epi_archive()
   )